In this thesis I aimed to provide base-line data to inform conservation of neotropical otters (Lontra longicaudis ) at both the range-wide and local (Mexico) scale. In Chapter 2, I compared three commonly used preservation methods for faecal DNA in order to identify the best method for neotropical otter faeces under challenging field conditions and long-term storage: 1) ambient-temperature drying, 2) a two-step protocol involving incubation in 95% ethanol and posterior silica desiccation, and 3) RNAlater. The results of this experiment showed that that RNAlater provides the highest mtDNA amplification success. In Chapter 3, I looked into the demographic history, genetic diversity and genetic structure of L. Longicaudis in Mexico using mtDNA. I found high genetic structure among North and South regions of the country, potentially due to geographic formations. Analyses of demographic history in Mexico indicated a recent expansion coinciding with the end of the Pleistocene. Given that recent evidence supports the existence of three subspecies of L. longicaudis across its range, I combined mtDNA haplotypes identified in this study with available Central and South American haplotypes in order to examine phylogeographic patterns; as a result, a distinct lineage distributed in North and Central America (NCAM) was identified. Due to the monophyly of this lineage, I propose to consider it a distinctive Evolutionary Significant Unit (ESU). In Chapter 4, I used landscape genetics to identify landscape features that affect otter geneflow in Mexico by means of microsatellites. I looked into the effect of elevation, slope, river networks and land cover on geneflow at a country-wide scale and two regional scales (North and South Pacific). I used Bayesian clustering to examine country-wide genetic structure. In terms of landscape genetics, elevation and slope were the only variables that explained genetic distance among individuals at the range-wide and North Pacific scale, respectively. The results of Bayesian clustering indicated two population clusters roughly distributed in the North and South of Mexico. The results of this thesis suggest that non-invasive methods can be applied to inform conservation efforts for Neotropical otters. I suggest that the NCAM lineage should be considered a distinct Evolutionary Significant Unit (ESU) throughout the range of L.longicaudis. Within Mexico, it is recommended to plan conservation corridors for the species where naturally low elevations and slopes allow genetic connectivity.